extract region from the bam file

Question

[9521ljh]

i have sorted *.bam file and i want to extract particular regions mapping

i have .bed file

chr2 179390716 179695529
chr3 89825161 90460254
chr8 144939497 144952632



samtools view -b -L .bed *.bam > output

the output file have only NNNNNNNN, there's no reads. what is the problem? i already check if there position have reads or not.

[WouterDeCoster]

.bed *.bam

These are your actual filenames?

[finswimmer]

Beside WouterDeCoster 's question: How have you checked the output?

[9521ljh]

Yes. the output just enumerate All NNNNNNNNNNNNNNNNNNNNNNN

[finswimmer]

I have asked for the command you used for checking the content and not how the content looks like :)

Also, please answer the question by Wouter.

[WouterDeCoster]

And another question: how did you get this bam file?

You'll need to share more information, we cannot guess what happened and cannot see your screen.